The aim of the study is to determine the distribution of trace and major elements in the water and in the sediments of the south part of the Bacalar Lagoon and to identify the sources of the trace elements and their changes over time. The western part of the lagoon water column is characterised by high concentrations of Ca2+, HCO3– and Sr2+, derived from groundwater input. In contrast, the eastern part of the lagoon is characterised by high concentrations of Mg2+, Na+ and Cl–. The lagoon is not affected by present-day seawater intrusion. Water column and sediment geochemical analyses performed in Bacalar Lagoon show clear spatial distribution of different parameters. The saturation index of the water column indicates three main groups: (1) a zone oversaturated with regard to aragonite, calcite and dolomite; (2) an undersaturated area where all three minerals are dissolving; and (3) an area with calcite equilibrium and undersaturation with regard to the other minerals. Herein we present the first measurements of trace element (Ba2+, Mn2+, K+, Ni2+, Zn2+) concentrations in carbonates obtained from sediments in Bacalar Lagoon. In order to evaluate whether the trace elements are derived from natural or anthropogenic sources, four pollution indices were calculated. The results confirmed that Bacalar Lagoon sediments are not contaminated with Ni2+, K+, Mn2+ and Ba2+, and that the Zn2+ seems to have a predominantly anthropogenic origin.